title: HN3: Uninfected Normal Liver Tissue (Small RNA-Seq)

city: Kolkata

first: Soma

last: Banerjee

state: West Bengal

address: 244, A.J.C Bose Road

department: School of Digestive & Liver Diseases

country: India

institute: Institute of Post Graduate Medical Education & Research

description:
HN3
Normal Liver Tissue from Gall Bladdar Carcinoma patients after verification of Liver Histology

data_processing:
The adaptors were trimmed using cutadapt tool.  A Phred score Q15 cut-off was applied for quality trimming, and reads less than 16 bases were also removed before downstream analysis.
Bowtie2 was used for mapping with the human genome hg19 as well as miRNAs in mirbase21. Reads were aligned locally with one base seed mismatch within a k-mer size of 19 bases. Samtools was used to assess the depth of coverage.
Differentially expressed miRNAs were obtained using DESeq2 packages in R software.
The ratios were log-converted (Log2) and the outliers in the Log2FC distribution (µ + 2σ / µ – 2σ) were used to identify over-expression and under-expression respectively. Minimum 5 reads and present in at least two of the samples were included to eliminate false positives.
Genome_build: hg19, mirbase21
Supplementary_files_format_and_content: Small RNA Sequences_non-normalized.xls

source_name: Liver Tissue

extract_protocol:
About 5 mg of liver tissues were powdered keeping frozen in liquid nitrogen and the total RNA was isolated using TRIzol (Invitrogen, CA) following the manufacturer's protocol. Quality of each RNA was verified using Bioanalyzer (Agilent, CA) and RNA integrity number (RIN) ≥6.5 was considered for Next Generation Sequencing (NGS).
Total RNA isolated from liver tissues were subjected to high throughput small RNA sequence analysis using Illumina HiSeq2500 in Medgenome Labs Private Limited, Bangalore, India. In brief, total RNA was ligated to 3’and 5’ adaptors, followed by reverse transcription and amplification using Truseq Small RNA Sample Prep Kit (Illumina, USA). The RNA fragment of length 145-160nt was gel purified to enrich small RNA library and sequenced.

value: Normal Liver Tissue

tag: etiology

value: Uninfected

tag: gender

value: Male


title: HCV-HCC-T2: Tumor Liver Tissue (Small RNA-Seq)

status: Public on Nov 15 2019

type: SRA

description:
HCV-HCC T2
Tumor tissue from orthotropic liver transplant of HCV infected HCC patients

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

value: HCC Tumor Tissue

value: HCV


title: HCV-HCC-T1: Tumor Liver Tissue (Small RNA-Seq)

description:
HCV-HCC T1
Tumor tissue from orthotropic liver transplant of HCV infected HCC patients


title: HCV-HCC-T4: Tumor Liver Tissue (Small RNA-Seq)

description:
HCV-HCC T4
Tumor tissue from orthotropic liver transplant of HCV infected HCC patients


title: S1: MCF10A-scramble shRNA rep1

city: Iowa City

first: Hank

last: Qi

state: IA

address: 1-632 Bowen Science Building

country: USA

institute: University of Iowa

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then pseudo-aligned using the kallisto method
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited tsv files including lengths, counts and transcripts per million (TPM) for mRNA transcripts

molecule: polyA RNA

growth_protocol: MCF10A cells were cultured in DMEM-F12 supplemented with 20 ng/ml Epidermal Growth Factor (EGF) (Sigma), 100 ng/ml cholera toxin (Sigma), 10 μg/ml insulin (Sigma), 500 ng/ml hydrocortisone (Sigma), and 5% horse serum. Cells were maintained in the specified medium supplemented with 1× Penicillin–Streptomycin (Gibco) and incubated in 5% CO2 at 37 °C.

extract_protocol:
Total RNA was isolated from MCF10A/control cells using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s protocol. RNA-seq libraries were made using the TruSeq Stranded Total RNA LT Sample Prep Kit (with Ribo-Zero™ Human/Mouse/Rat, RS-122-2201) and multiplexed with Illumina barcodes. Two biological duplicates of MCF10A/control samples, HER2 overexpression and two constructs of shRNA PHF8 were sequenced on the HiSeq2500 instrument following protocols supplied by Illumina (San Diego, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols. 50-bp paired-end reads were generated. More than 20 Mb reads were produced for each library.

tag: origin

value: Mammary Epithelial Cells

tag: cell line

tag: cell type

value: breast cancer


title: sgLacZ treated neurons_2

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

data_processing:
Fastq files were mapped to the mm10 mouse reference genome with the STAR aligner v2.7 (Dobin et al., 2013).
Differential gene expression and Functional enrichment analyses were performed with DESeq2 (Love et al., 2014) and GSEA (Huang et al., 2009), respectively.
Statistical and downstream bioinformatics analyses were performed within the R environment.
Gene expression heatmaps were produced with GENE-E (Broad Institute).
Genome_build: mm10
Supplementary_files_format_and_content: featureCounts gene counts

organism: Mus musculus

source_name: Primary hippocampal neurons

extract_protocol:
RNA was isolated with Trizol (Thermo Fisher), and treated with DNase I (NEB) according to manufacturer's instructions.
Library preparation was done with QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) according to manufacturer's instructions.

tag: treatment

value: sgLacZ

tag: genotype

value: control

value: brain

tag: tissue region

value: hippocampus

value: primary neurons


title: sgKcna1 treated neurons_1

value: CRISPRa-mediated Kv1.1 upregulation


title: sgKcna1 treated neurons_3


title: HN2: Uninfected Normal Liver Tissue (Small RNA-Seq)

description:
HN2
Normal Liver Tissue from Gall Bladdar Carcinoma patients after verification of Liver Histology


title: sgLacZ treated neurons_1


title: PA43653_TAGCTT_L006

city: Houston

first: Stephanie

last: Pangas

address: One Baylor College of Medicine

department: Pathology & Immunology

institute: Baylor College of Medicine

description: 1 ovary each from 3 Ubc9flox/flox Gdf9iCre+ mice were pooled

data_processing:
Reads were mapped with TopHat 2.0. Only uniquely mapping reads were kept
The mapped reads were quantified with Cufflinks 2.0 and the GENCODE gene model.
Gene expression (FPKM) was quantile normalized using the R statistical system.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each Sample

source_name: ovarian tissue

extract_protocol:
One ovary each from three Ubc9f/f control or Ubc9f/f Gdf9iCre+ mice were pooled per biological replicate (N = 3 per genotype) with the same amount of total RNA. Ovaries were removed and stored in RNA later (Life Technologies) until RNA extraction.  RNA was harvested using the RNeasy micro kit (Qiagen). RNA-sequencing was performed on an Illumina HiSeq 2500 system.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ovary

tag: strain

tag: age

value: postnatal day 14

value: Ubc9flox/flox Gdf9iCre+


title: PA43661_GGCTAC_L006


title: HN1: Uninfected Normal Liver Tissue (Small RNA-Seq)

description:
HN1
Normal Liver Tissue from Gall Bladdar Carcinoma patients after verification of Liver Histology


title: PA43451_ACTTGA_L006

description: 1 ovary each from 3 Ubc9flox/flox mice were pooled


title: PA43447_TTAGGC_L006


title: PA43455_GATCAG_L006


title: Pl_CxFi_++_3

city: Munich

first: Daniel

last: Andergassen

address: Biedersteiner Straße 29

country: Germany

institute: Technical University Munich

description:
procesed data file:
Pl_CxFi_++_3.bw

data_processing:
RNA sequencing data was aligned to the mm10 genome using STAR (version 2.5.0c). Reads mapping to multiple locations were excluded using specific parameters (STAR:--outFilterMultimapNmax 1). Additional parameters for the STAR alignment were a maximum intron size of 100,000 bp and out-filtering of non-canonical splice junctions.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: extraembryonic placenta

extract_protocol:
RNA was extracted from TRIzol using standard protocols.
The Illumina TruSeq kit was used to create polyA+ libraries from total RNA. We generated strand-specific libraries for tissues collected form the F1 crosses (TruSeq stranded Illumina) and non-strand-specific TruSeq libraries for the adult organs. All the libraries were run on a Bioanalyzer to assess purity, fragment size, and concentration and sequenced on a HiSeq 2500 at Harvard University’s Bauer Sequencing Core (75 bp paired end).

value: extraembryonic placenta

tag: background (maternal x paternal for hybrids)

value: Firre

tag: genotype  (left position=maternal; right position=paternal)

tag: Sex

value: F


title: PA43446_ATCACG_L006


title: Pl_CxFi_++_1

description:
procesed data file:
Pl_CxFi_++_1.bw


title: sgKcna1 treated neurons_2


title: Pl_CxFi_+-_3

description:
procesed data file:
Pl_CxFi_+-_3.bw


title: Pl_CxFi_+-_2

description:
procesed data file:
Pl_CxFi_+-_2.bw


title: Pl_CxFi_+-_1

description:
procesed data file:
Pl_CxFi_+-_1.bw


title: Pl_CxDF_++_1

description:
procesed data file:
Pl_CxDF_++_1.bw


title: Pl_CxDF_++_3

description:
procesed data file:
Pl_CxDF_++_3.bw


title: Pl_CxDF_++_2

description:
procesed data file:
Pl_CxDF_++_2.bw


title: Pl_CxDF_+-_2

description:
procesed data file:
Pl_CxDF_+-_2.bw


title: Pl_CxD_++_3

description:
procesed data file:
Pl_CxD_++_3.bw


title: Pl_CxDF_+-_1

description:
procesed data file:
Pl_CxDF_+-_1.bw


title: Pl_CxDF_+-_3

description:
procesed data file:
Pl_CxDF_+-_3.bw


title: Pl_CxD_+-_3

description:
procesed data file:
Pl_CxD_+-_3.bw


title: Pl_FixC_+y_3

description:
procesed data file:
Pl_FixC_+y_3.bw

value: +y

value: M


title: Pl_CxD_+-_1

description:
procesed data file:
Pl_CxD_+-_1.bw


title: Pl_CxD_++_1

description:
procesed data file:
Pl_CxD_++_1.bw


title: Pl_CxD_+-_2

description:
procesed data file:
Pl_CxD_+-_2.bw


title: Pl_FixC_+y_2

description:
procesed data file:
Pl_FixC_+y_2.bw


title: patient #1 C-Mo

type: RNA

city: Buffalo

first: Jason

last: Muhitch

state: NY

address: Elm & Carlton Sts.

department: Urology

institute: Roswell Park Cancer Institute

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: The data were quantile normalized in R

label: biotin

source_name: classical monocytes

label_protocol: standard Illumina protocol

extract_protocol: RNA was extracted with Trizol reagent.

tag: disease state

value: renal cell carcinoma

tag: monocyte subset

value: classical


title: Pl_CxFi_++_2

description:
procesed data file:
Pl_CxFi_++_2.bw


title: SCR replicat 1 RNAseq

city: Toulouse

first: Aude

last: Guenole

address: Université de Toulouse, UT3, Toulouse 31062, France

department: Centre de Biologie Integrative

country: France

institute: CNRS

description:
Stranded_mRNA
Index: ATCACG (Illumina)

data_processing:
The libraries are mapped using Bowtie 2.0.5 and TopHat  2.0.6 to the reference
Expression estimation, normalization and comparison where done using the Cufflinks v2.1.1  program.
Cuffdiff  then  uses  the  Cufflinks  transcript  quantification  engine  to  calculate  gene  and  transcript expression levels in more than one condition and tests them for significant differences. It can find differentially  expressed  genes  and  transcripts,  as  well  as  genes  that  are  being  differentially regulatedat the transcriptional and post-transcriptional levels.
3 contrôle (CTRL) triplicate  are consider as Sample1 (SCR) . The 2 SiRNA replicate are consider as Sample2 (Si-CDS RNF219). The 2 Si-UTR RNF219 replicates are considered as Sample 3 (Si-UTR2 RNF219).
Scr is compared to Si-CDS RNF219  and Scr is compared to Si-UTR2 RNF219. All data are contained within the file RNAseq-SCR-vs-SiRNF219_hg38_gene_exp_diff-Only-v3.csv
Genome_build: hg38
Supplementary_files_format_and_content: tab/semi-colons separated fields, with a header line to define each column
Supplementary_files_format_and_content: test_id: A unique identifier describing the transcript or gene being tested
Supplementary_files_format_and_content: gene_id: The gene_id being tested
Supplementary_files_format_and_content: gene: The gene_name being tested
Supplementary_files_format_and_content: locus: Genomic coordinates of the transcript or gene being tested
Supplementary_files_format_and_content: sample1:first group in the comparison
Supplementary_files_format_and_content: sample2: second group in the comparison
Supplementary_files_format_and_content: status: can be one of:
Supplementary_files_format_and_content: ? OK (test successful)
Supplementary_files_format_and_content: ? NOTEST (not enough alignments for testing)
Supplementary_files_format_and_content: ? LOWDATA (too complex or shallowly sequenced)
Supplementary_files_format_and_content: ? HIDATA (too many fragments in locus)
Supplementary_files_format_and_content: ? FAIL (when an ill-conditioned covariance matrix or other numerical exception prevents testing)
Supplementary_files_format_and_content: value columns:FPKMs of the transcript or gene in each group
Supplementary_files_format_and_content: log2(FPKM/FPKM): the (base 2) log of the fold change between 2 groups
Supplementary_files_format_and_content: test stat:significance of the observed change of FPKM
Supplementary_files_format_and_content: pvalue:uncorrected p-value of the test statistic
Supplementary_files_format_and_content: qvalue:FDR-adjusted p-value of the test statistic
Supplementary_files_format_and_content: significant: can be either yes or no, depending on whether p is greater than the FDR after Bengamini-Hochberg correction for multiple-testing

source_name: Hela

growth_protocol: Hela cell grow in DMEM + 10% FBS and 1% Pen/Strep. All cells were incubated at 37°C in 5% CO2

extract_protocol:
Total RNA with Trizol extraction. Total RNA was enriched for the Poly-A mRNA
Illumina Stranded RNA

treatment_protocol: Cells were grown to 50-60% confluence before Si RNA transfection with Fugen. Medium is wash after 8H hour and cells collected 48h hour after transfection

value: Hela

tag: sirna

value: SCR


title: Pl_FixC_+y_1

description:
procesed data file:
Pl_FixC_+y_1.bw


title: Pl_FixC_++_3

description:
procesed data file:
Pl_FixC_++_3.bw


title: Si CDS RNF219 replicat 2 RNAseq

description:
Stranded_mRNA
Index: TAGCTT (Illumina)

value: Si RNF219


title: Si CDS RNF219 replicat 1 RNAseq

description:
Stranded_mRNA
Index: CGATGT (Illumina)


title: Pl_FixC_++_1

description:
procesed data file:
Pl_FixC_++_1.bw


title: Pl_FixC_++_2

description:
procesed data file:
Pl_FixC_++_2.bw


title: SCR replicat 2 RNAseq

description:
Stranded_mRNA
Index: CAGATC (Illumina)


title: BL3X01_02

city: Bethesda

first: Sijung

last: Yun

state: Maryland

address: 8908 Ewing Drive

institute: NIH/JHU

data_processing:
An accuracy of Q30 or higher was achieved in 94.95% of base calls. A total of 52.2 -75.5 million read counts were performed for each sample. Bioinformatics QC was performed using FastQC, version 0.11.5; both before and after moderate blast all samples met QC criteria for sufficient integrity based on RNA Integrity Number, and were sequenced.
Spliced Transcript Alignment to a Reference (STAR) version 2.5, was used to align to the hg19 reference genome.
The number of reads mapped to gene were counted using HTSEQ version 0.6.1p1.
Differentially expressed genes were identified using DESeq2 version 1.12.3; the cutoff for false discovery rate was set to 0.10.
Genome_build: hg19

source_name: Blood

extract_protocol:
Blood was drawn on each training day between 1600 and 1800 hours, processed for serum, and stored at -80 ° C until batch processing. PAXgene™ tubes were collected at baseline; in the moderate blast-exposed participants, PAXgene™ tubes were also collected on the last day of training (day 10) to establish gene expression changes from baseline. Tubes were inverted 8-10 times and were sat upright for at least 2 hours (but no more than 72 hours) at room temperature, at which point they were then moved to a -20 o C freezer for at least 24 hours; finally, samples were transferred to a -80 o C freezer until batch processing.
A cDNA library was prepared by random fragmentation of the cDNA followed by 5’ and 3’ adapter ligation. Briefly, a High Capacity Reverse Transcription Kit (Applied Biosystems, Foster City, CA) was used to synthesize cDNA from 10µl of total RNA. One-tenth diluted cDNA was mixed with TaqMan assay-on- demand and TaqMan gene expression master mix solution (Applied Biosystems, Foster City, CA). Triplicate reactions each totaling 6µl were analyzed using qPCR (QuantStudio 6 Flex, Thermo Fisher Scientific, Waltham, MA); the data was processed with QuantStudio Real-Time PCR Software version 1.1 (Applied Biosystems, Foster City, CA).

tag: time point

value: base line


title: BL3F05_10

value: 10 days


title: BL3X01_10


title: BL3F05_01


title: BL3F04_10


title: Pl_FixC_-y_2

description:
procesed data file:
Pl_FixC_-y_2.bw

value: -y


title: Pl_FixC_-y_1

description:
procesed data file:
Pl_FixC_-y_1.bw


title: Pl_FixC_-+_3

description:
procesed data file:
Pl_FixC_-+_3.bw


title: Pl_CxD_++_2

description:
procesed data file:
Pl_CxD_++_2.bw


title: Pl_FixC_-+_2

description:
procesed data file:
Pl_FixC_-+_2.bw


title: BL3F04_01


title: BL3F01_10


title: Pl_FixC_-+_1

description:
procesed data file:
Pl_FixC_-+_1.bw


title: BL3F02_01


title: Pl_DxC_+y_3

description:
procesed data file:
Pl_DxC_+y_3.bw


title: BL3F01_01


title: Pl_DxC_+y_1

description:
procesed data file:
Pl_DxC_+y_1.bw


title: Pl_FixC_-y_3

description:
procesed data file:
Pl_FixC_-y_3.bw


title: Pl_DxC_++_1

description:
procesed data file:
Pl_DxC_++_1.bw


title: BL3E05_01


title: Pl_DxC_-y_3

description:
procesed data file:
Pl_DxC_-y_3.bw


title: Pl_DxC_++_2

description:
procesed data file:
Pl_DxC_++_2.bw


title: BL3E04_01


title: BL3E04_10


title: BL3E03_01


title: Pl_DxC_-+_3

description:
procesed data file:
Pl_DxC_-+_3.bw


title: Pl_DxC_-y_1

description:
procesed data file:
Pl_DxC_-y_1.bw


title: BL3E03_10


title: Pl_DxC_-+_2

description:
procesed data file:
Pl_DxC_-+_2.bw


title: Pl_DFxC_+y_3

description:
procesed data file:
Pl_DFxC_+y_3.bw


title: BL3E02_01


title: BL3E02_10


title: BL3E01_01


title: Pl_DxC_-+_1

description:
procesed data file:
Pl_DxC_-+_1.bw


title: BL3E01_10


title: Pl_DxC_+y_2

description:
procesed data file:
Pl_DxC_+y_2.bw


title: Pl_DFxC_+y_2

description:
procesed data file:
Pl_DFxC_+y_2.bw


title: BL3F02_10


title: BL3D05_10


title: patient #5 C-Mo


title: BL3E05_10


title: BL3D04_10


title: Pl_DFxC_++_3

description:
procesed data file:
Pl_DFxC_++_3.bw


title: Pl_DxC_-y_2

description:
procesed data file:
Pl_DxC_-y_2.bw


title: Pl_DFxC_++_2

description:
procesed data file:
Pl_DFxC_++_2.bw


title: BL3D04_01


title: BL3D03_10


title: Pl_DFxC_-y_2

description:
procesed data file:
Pl_DFxC_-y_2.bw


title: BL3D02_10


title: Pl_DFxC_-y_3

description:
procesed data file:
Pl_DFxC_-y_3.bw


title: Pl_DFxC_-y_1

description:
procesed data file:
Pl_DFxC_-y_1.bw


title: BL3D03_01


title: BL3D02_01


title: Pl_DFxC_-+_3

description:
procesed data file:
Pl_DFxC_-+_3.bw


title: Pl_DFxC_-+_1

description:
procesed data file:
Pl_DFxC_-+_1.bw


title: Pl_DFxC_-+_2

description:
procesed data file:
Pl_DFxC_-+_2.bw


title: BL3D01_01


title: BL3D01_10


title: Pl_DFxC_+y_1

description:
procesed data file:
Pl_DFxC_+y_1.bw


title: BL3C05_01


title: BL3D05_01


title: Br_CxFi_++_2

description:
procesed data file:
Br_CxFi_++_2.bw

source_name: embryonic brain

value: embryonic brain


title: Br_CxFi_++_1

description:
procesed data file:
Br_CxFi_++_1.bw


title: BL3C04_10


title: Br_CxFi_+-_3

description:
procesed data file:
Br_CxFi_+-_3.bw


title: BL3C03_10


title: Br_CxFi_+-_2

description:
procesed data file:
Br_CxFi_+-_2.bw


title: Pl_DFxC_++_1

description:
procesed data file:
Pl_DFxC_++_1.bw


title: Br_CxFi_+-_1

description:
procesed data file:
Br_CxFi_+-_1.bw


title: BL3C03_01


title: BL3C04_01


title: BL3C02_01


title: Br_CxDF_+-_3

description:
procesed data file:
Br_CxDF_+-_3.bw


title: Br_CxDF_++_1

description:
procesed data file:
Br_CxDF_++_1.bw


title: BL3C01_01


title: BL3C05_10


title: Br_CxFi_++_3

description:
procesed data file:
Br_CxFi_++_3.bw


title: BL3B05_10


title: BL3C02_10


title: Br_CxDF_+-_1

description:
procesed data file:
Br_CxDF_+-_1.bw


title: BL3B04_01


title: Br_CxD_++_3

description:
procesed data file:
Br_CxD_++_3.bw


title: BL3B05_01


title: BL3B02_10


title: Br_CxD_++_2

description:
procesed data file:
Br_CxD_++_2.bw


title: Br_CxD_++_1

description:
procesed data file:
Br_CxD_++_1.bw


title: BL3B02_01


title: Br_CxD_+-_2

description:
procesed data file:
Br_CxD_+-_2.bw


title: Br_CxD_+-_1

description:
procesed data file:
Br_CxD_+-_1.bw


title: BL3B01_01


title: Br_CxDF_++_2

description:
procesed data file:
Br_CxDF_++_2.bw


title: Br_FixC_+y_3

description:
procesed data file:
Br_FixC_+y_3.bw


title: Br_CxDF_++_3

description:
procesed data file:
Br_CxDF_++_3.bw


title: Br_CxD_+-_3

description:
procesed data file:
Br_CxD_+-_3.bw


title: BL3A05_10


title: BL3C01_10


title: Br_CxDF_+-_2

description:
procesed data file:
Br_CxDF_+-_2.bw


title: Br_FixC_+y_2

description:
procesed data file:
Br_FixC_+y_2.bw


title: BL3A04_01


title: BL3A05_01


title: BL3B04_10


title: Br_FixC_++_3

description:
procesed data file:
Br_FixC_++_3.bw


title: BL3A03_01


title: Br_FixC_++_2

description:
procesed data file:
Br_FixC_++_2.bw


title: BL3A03_10


title: Br_FixC_+y_1

description:
procesed data file:
Br_FixC_+y_1.bw


title: Br_FixC_++_1

description:
procesed data file:
Br_FixC_++_1.bw


title: BL3A02_10


title: BL3A01_10


title: Br_FixC_-y_2

description:
procesed data file:
Br_FixC_-y_2.bw


title: Br_FixC_-y_3

description:
procesed data file:
Br_FixC_-y_3.bw


title: BL3B01_10


title: Br_FixC_-+_3

description:
procesed data file:
Br_FixC_-+_3.bw


title: Br_FixC_-y_1

description:
procesed data file:
Br_FixC_-y_1.bw


title: Br_FixC_-+_2

description:
procesed data file:
Br_FixC_-+_2.bw


title: BL3A01_01


title: Br_DxC_+y_3

description:
procesed data file:
Br_DxC_+y_3.bw


title: Br_DxC_++_2

description:
procesed data file:
Br_DxC_++_2.bw


title: Br_DxC_+y_1

description:
procesed data file:
Br_DxC_+y_1.bw


title: Br_FixC_-+_1

description:
procesed data file:
Br_FixC_-+_1.bw


title: BL3A04_10


title: Br_DxC_+y_2

description:
procesed data file:
Br_DxC_+y_2.bw


title: Br_DxC_++_1

description:
procesed data file:
Br_DxC_++_1.bw


title: Br_DxC_-y_2

description:
procesed data file:
Br_DxC_-y_2.bw


title: Br_DxC_-y_1

description:
procesed data file:
Br_DxC_-y_1.bw


title: Br_DxC_-+_2

description:
procesed data file:
Br_DxC_-+_2.bw


title: Br_DxC_-+_1

description:
procesed data file:
Br_DxC_-+_1.bw


title: N722_S503_6 scRNAseq

city: Stockholm

first: Marcus

last: Buggert

state: PA

address: C2:94; Karolinska Universitetssjukhuset Huddinge

department: Microbiology

country: Sweden

institute: Karolinska Institutet

data_processing:
Paired-end sequencing reads were then trimmed to remove adaptor sequences and low-quality basecalls using the utility Trimmomatic
 Reads were subsequently aligned using Bowtie against a genomic repeat element database derived from RepeatMasker software to quantify and remove transcript reads considered to be irrelevant for the analysis in hand (rRNA, rRNA, LINEs, SINEs, etc
 The remaining reads were aligned against the most recent human genome build, hg38, using the splice-site aware aligner, STAR
Transcripts were then quantified and normalized using the bioinformatics package, Cufflinks
Genome_build: hg38

extract_protocol: Libraries were prepared by getting mRNA be reverse transcribed from an anchored oligo-dT primer that includes a universal priming site at the 5’ end. RT reactions also included a template-switch oligonucleotide to allow the incorporation of the universal priming site at cDNA 3’ ends. Whole transcriptome cDNA was then amplified by PCR for 22–24 cycles using universal priming sites primers and Kapa HiFi Hot Start ReadyMix. After post-PCR clean-up, amplified whole transcriptome cDNA was incorporated into barcoded Illumina Nextera libraries and sequenced to a depth of about 2 million 150bp paired-end reads/cell on a HiSeq 4000 (Illumina).  and amplified for 14 PCR cycles. Libraries were pooled and paired-end sequenced (38bp+37bp).

value: Lymph node

tag: passages

value: FACS purified cells


title: BL3A02_01


title: N721_S511_6 scRNAseq

tag: tissue


title: N722_S502_6 scRNAseq


title: N722_S507_6 scRNAseq


title: N722_S505_6 scRNAseq


title: Br_DFxC_+y_3

description:
procesed data file:
Br_DFxC_+y_3.bw


title: Br_DxC_-+_3

description:
procesed data file:
Br_DxC_-+_3.bw


title: N721_S507_6 scRNAseq


title: N721_S508_6 scRNAseq


title: Br_DFxC_+y_2

description:
procesed data file:
Br_DFxC_+y_2.bw


title: Br_DFxC_+y_1

description:
procesed data file:
Br_DFxC_+y_1.bw


title: Br_DFxC_++_3

description:
procesed data file:
Br_DFxC_++_3.bw


title: N721_S505_6 scRNAseq


title: N721_S506_6 scRNAseq


title: Br_DFxC_++_2

description:
procesed data file:
Br_DFxC_++_2.bw


title: Br_DFxC_++_1

description:
procesed data file:
Br_DFxC_++_1.bw


title: N721_S503_6 scRNAseq


title: Br_DxC_-y_3

description:
procesed data file:
Br_DxC_-y_3.bw


title: N720_S511_6 scRNAseq


title: N720_S510_6 scRNAseq


title: Br_DFxC_-y_3

description:
procesed data file:
Br_DFxC_-y_3.bw


title: Br_DFxC_-y_1

description:
procesed data file:
Br_DFxC_-y_1.bw


title: Br_DFxC_-y_2

description:
procesed data file:
Br_DFxC_-y_2.bw


title: N720_S508_6 scRNAseq


title: N720_S507_6 scRNAseq


title: N721_S510_6 scRNAseq


title: N720_S506_6 scRNAseq


title: Br_DFxC_-+_2

description:
procesed data file:
Br_DFxC_-+_2.bw


title: N720_S505_6 scRNAseq


title: Br_DFxC_-+_3

description:
procesed data file:
Br_DFxC_-+_3.bw


title: Br_DFxC_-+_1

description:
procesed data file:
Br_DFxC_-+_1.bw


title: Sp_FixFi_--_2

description:
procesed data file:
Sp_FixFi_--_2.bw

source_name: adult spleen

value: adult spleen

value: 6 weeks


title: N720_S503_6 scRNAseq


title: Sp_DxD_--_2

description:
procesed data file:
Sp_DxD_--_2.bw


title: Sp_FixFi_--_3

description:
procesed data file:
Sp_FixFi_--_3.bw


title: N719_S508_6 scRNAseq


title: N719_S510_6 scRNAseq


title: N719_S507_6 scRNAseq


title: N719_S506_6 scRNAseq


title: N719_S505_6 scRNAseq


title: Sp_DFxDF_++_4

description:
procesed data file:
Sp_DFxDF_++_4.bw


title: N718_S511_6 scRNAseq


title: Sp_DFxDF_++_2

description:
procesed data file:
Sp_DFxDF_++_2.bw


title: N719_S502_6 scRNAseq


title: Sp_DxD_--_1

description:
procesed data file:
Sp_DxD_--_1.bw


title: MEF_Erastin_rep3

city: Sendai

first: Mitsuyo

last: Matsumoto

address: 2-1 Seiryo-machi Aoba-ku

department: Biochemistry

country: Japan

institute: Tohoku university school of medicine

description: Sample 16

data_processing:
Alignment of reads to reference mm10 were performed using the RNASeqAnalysis plugin from the Ion torrent suite software. Files format of final downloaded data (raw data) from Ion Proton was BAM.
Read counts were performed using Htseq version 0.9.1 htseq-count (samtools view -F4 [raw_file(BAM)] | htseq-count -q -t exon -I gene_id - mm10.gtf).
Genome_build: mm10
Supplementary_files_format_and_content: txt (Matrix data containing read counts data of all sample: Out put file was generated from "data processing step")

source_name: primary MEF

growth_protocol: Primary MEFs were prepared and maintained at 37ºC in Dulbecco’s modified Eagle medium (Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS) (JRH Bioscience, Levexa, KS, USA), 0.1 mM nonessential amino acids (Invitrogen), penicillin/streptomycin (10,000 U/ml each, Invitrogen) and 55 mM 2-mercaptoethanol (Wako Pure Chemicals, Osaka, Japan)

extract_protocol:
The cells were harvested by centrifugation, and the total RNA was isolated using a RNeasy Plus Mini kit (QIAGEN) following the instruction manual. Four microgram of total RNA was treated using a GeneRead rRNA Depletion kit (Qiagen) for remove Ribosomal RNA (rRNA) and an RNeasy MiniElute kit (Qiagen) for cleanup. One hundred ng of rRNA-depleted RNA was incubated at 95 ºC for 10 min for fragmentation and was purified by Magnetic Beads Cleanup Module (Life Technologies).
The libraries were constructed using Ion Total RNA-seq kit for AB Libraly builer system (Thermo Fisher Scientific Inc.) and were barcoded with Ion Xpress RNA-seq BC primer ((Thermo Fisher Scientific Inc., 16 PCR cycles). Barcoded library fragment with the size range of 100-200 bp was selected with Agencourt AMPure XP beads (Beckman Coulter, Brea, CA). Templates were prepared using Ion PI Hi-Q Chef Kit (Thermo Fisher Scientific Inc.) on Ion Chef (Thermo Fisher Scientific Inc.). Sequencing was performed on an Ion Proton system by the P1 chip v3 (Thermo Fisher Scientific Inc.) using Hi-Q Sequensing kit  (Thermo Fisher Scientific Inc.).

treatment_protocol: MEFs (9th passages) were exposed to 3 µM erastin. 24 hours later, the cells were harvested for RNA isolation.

value: primary Mouse Embryonic Fibroblast

value: 3 µM Erastin


title: Sp_DFxDF_++_1

description:
procesed data file:
Sp_DFxDF_++_1.bw

value: F


title: MEF_Erastin_rep1

description: Sample 14


title: N719_S511_6 scRNAseq


title: MEF_DMSO_rep3

description: Sample 13

value: DMSO


title: Sp_FixFi_--_1

description:
procesed data file:
Sp_FixFi_--_1.bw


title: MEF_DMSO_rep2

description: Sample 12


title: Sp_DFxDF_--_2

description:
procesed data file:
Sp_DFxDF_--_2.bw


title: Sp_DFxDF_--_3

description:
procesed data file:
Sp_DFxDF_--_3.bw


title: N718_S505_6 scRNAseq


title: N718_S506_6 scRNAseq


title: MEF_Erastin_rep2

description: Sample 15


title: MEF_DMSO_rep1

description: Sample 11


title: Sp_DFxDF_--_1

description:
procesed data file:
Sp_DFxDF_--_1.bw


title: Sp_DFxDF_++_3

description:
procesed data file:
Sp_DFxDF_++_3.bw


title: N718_S508_6 scRNAseq


title: N718_S502_6 scRNAseq


title: Lu_DFxDF_++_4

description:
procesed data file:
Lu_DFxDF_++_4.bw

source_name: adult lung

value: adult lung


title: sgLacZ treated neurons_3

value: sgLacZ

value: control

value: brain

value: hippocampus

value: primary neurons


title: Sp_DFxDF_--_4

description:
procesed data file:
Sp_DFxDF_--_4.bw


title: N716_S511_6 scRNAseq


title: Lu_DFxDF_++_3

description:
procesed data file:
Lu_DFxDF_++_3.bw


title: Lu_DFxDF_++_2

description:
procesed data file:
Lu_DFxDF_++_2.bw


title: N716_S510_6 scRNAseq


title: Lu_DFxDF_++_1

description:
procesed data file:
Lu_DFxDF_++_1.bw


title: N716_S505_6 scRNAseq


title: N716_S503_6 scRNAseq


title: Lu_DFxDF_--_4

description:
procesed data file:
Lu_DFxDF_--_4.bw


title: N716_S502_6 scRNAseq


title: Lu_DFxDF_--_3

description:
procesed data file:
Lu_DFxDF_--_3.bw


title: Lu_DFxDF_--_2

description:
procesed data file:
Lu_DFxDF_--_2.bw


title: N729_S505_5 scRNAseq


title: Lu_DFxDF_--_1

description:
procesed data file:
Lu_DFxDF_--_1.bw


title: N729_S503_5 scRNAseq


title: Li_FixFi_--_3

description:
procesed data file:
Li_FixFi_--_3.bw

source_name: adult liver

value: adult liver


title: N718_S507_6 scRNAseq


title: KMJR138_DMSO_8h_rep2

city: Camperdown

first: Stuart

middle: J

last: Gallagher

state: NSW

address: Building 93, RPA Hospital

department: Melanoma Oncology

country: Australia

institute: Centenary Institute

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Genome Studio was used to generate non-normalized and non-background normalized values from idat files. These data were used to generate normalized data using the limma version 3.38.3 package in R version 3.5.3. using normal-exponential deconvolution method.

source_name: Melanoma

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal calf serum (FCS; AusGeneX, Brisbane, Qld, Australia) and Pen/Strep (Sigma, St Louis, MO, USA).

extract_protocol: Cells were scraped from flasks, washed in PBS and pelleted by centrifugation. Pellets were lysed in TRIzol reagent (Invitrogen) and purified with an RNeasy purification kit (Qiagen) with DNAse I digestion on the column, and the RNA quality was verified using the Agilent 2100 Bioanalyser (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Cells were seeded in 75 cm2 flasks in duplicate and treated the following day with DMSO or 7.5 μM GSK126. Following 8 and 48 hr incubation, cells were harvested.

tag: time


title: N728_S510_5 scRNAseq


title: N718_S503_6 scRNAseq


title: IGR-1_GSK126_48h_rep2

tag: cell line


title: IGR-1_DMSO_48h_rep2


title: Li_FixFi_--_2

description:
procesed data file:
Li_FixFi_--_2.bw

value: Firre


title: KMJR138_GSK126_8h_rep2


title: MelRMU_GSK126_8h_rep1

value: MelRMU


title: KMJR138_GSK126_48h_rep2


title: IGR-1_DMSO_8h_rep2


title: MelRMU_DMSO_8h_rep1


title: MelRMU_DMSO_48h_rep1


title: N728_S508_5 scRNAseq

value: Lymph node


title: KMJR138_DMSO_48h_rep2


title: MelRMU_GSK126_48h_rep1


title: MM386_GSK126_48h_rep1


title: Li_FixFi_--_1

description:
procesed data file:
Li_FixFi_--_1.bw


title: N728_S507_5 scRNAseq

value: FACS purified cells


title: MM386_DMSO_48h_rep1


title: IGR-1_GSK126_8h_rep2


title: N728_S505_5 scRNAseq


title: Li_DxD_--_1

description:
procesed data file:
Li_DxD_--_1.bw


title: Li_DFxDF_++_4

description:
procesed data file:
Li_DFxDF_++_4.bw


title: N727_S510_5 scRNAseq


title: Li_DxD_--_2

description:
procesed data file:
Li_DxD_--_2.bw


title: N727_S511_5 scRNAseq


title: N727_S507_5 scRNAseq


title: Li_DFxDF_++_3

description:
procesed data file:
Li_DFxDF_++_3.bw


title: MM386_GSK126_8h_rep1


title: MelRMU_GSK126_8h_rep2


title: MM386_GSK126_48h_rep2


title: MelRMU_GSK126_48h_rep2


title: MM386_GSK126_8h_rep2


title: Li_DFxDF_++_2

description:
procesed data file:
Li_DFxDF_++_2.bw


title: MM386_DMSO_8h_rep1


title: KMJR138_GSK126_48h_rep1


title: N726_S510_5 scRNAseq


title: MelRMU_DMSO_48h_rep2


title: Li_DFxDF_++_1

description:
procesed data file:
Li_DFxDF_++_1.bw


title: MAC_Camb_D3

type: genomic

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

description:
202163550095_R08C01
CD14 cells treated with M-CSF for 5 days in the presence of 50µM cambinol donor 3

hyb_protocol: BS-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (Illumina HiSeq2000) using standard recommended Illumina scanner setting

data_processing:
Data were processed using R studio;
methylated signal intensities is provided in the 'non_normalized.txt'

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

growth_protocol: Monocytes were isolated from buffy coats by CD14 positive selection (MACS) and differentiated with the addition of 25 ng/ml of human M-CSF (PeproTech) for 5 days in the presence of 0.1 % DMSO or 50 µM cambinol

extract_protocol: Total DNA was extracted by the proteinase K protocol.

treatment_protocol: 0.1 % DMSO or 50 µM cambinol were added from day 1 until day 5 of culture

tag: donor

value: donor 3

tag: cell type

value: M-CSF macrophages


title: MM386_DMSO_8h_rep2

tag: treatment


title: MAC_DMSO_D2

description:
202163550097_R07C01
CD14 cells treated with M-CSF for 5 days in the presence of 0.1 % DMSO donor 2

value: donor 2


title: MM386_DMSO_48h_rep2


title: IGR-1_DMSO_48h_rep1


title: Li_DFxDF_--_3

description:
procesed data file:
Li_DFxDF_--_3.bw

value: 6 weeks


title: MelRMU_DMSO_8h_rep2


title: N726_S507_5 scRNAseq


title: N726_S505_5 scRNAseq


title: Dnmt1 KO rep2

city: Freiburg

first: Nicola

last: Wanner

address: Breisacherstraße 66

department: Renal Division

institute: University Medical Center Freiburg

data_processing:
Fastq reads were pseudoaligned to the mm10 genome assembly using Kallisto (Bray et al., 2016) and transcript read counts were aggregated to Ensembl Gene IDs for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: plain text file of the abundance estimates, including estimated counts, TPM, effective length

source_name: Cap Mesenchyme

extract_protocol:
RNA from E18.5 sorted CM (n=3) was extracted using the chloroform/phenol method. 50 ng were sent to the DKFZ (Heidelberg) for Ultra Low RNA sequencing on an Illumina HiSeq2000 instrument.
Library preparation was performed by the DKFZ High Throughput Sequencing Unit

value: Cap Mesenchyme

value: kidney

value: embryonic day 18.5

tag: genotype

value: Dnmt1 -/-


title: Dnmt1 KO rep1

tag: strain


title: N726_S503_5 scRNAseq


title: Dnmt1 KO rep3

tag: age


title: KMJR138_GSK126_8h_rep1


title: Li_DFxDF_--_2

description:
procesed data file:
Li_DFxDF_--_2.bw

tag: background (maternal x paternal for hybrids)

value: F


title: Dnmt1 HET rep3

value: Dnmt1 +/-


title: KMJR138_DMSO_48h_rep1

value: DMSO


title: MAC_Camb_D2

description:
202163550097_R06C01
CD14 cells treated with M-CSF for 5 days in the presence of 50µM cambinol donor 2


title: MO_D1

description:
202163550095_R07C01
peripheral blood isolated CD14+ cells (monocytes) donor 1

value: donor 1

value: Monocytes


title: IGR-1_GSK126_48h_rep1


title: IGR-1_GSK126_8h_rep1


title: MAC_Camb_D1

description:
202163550097_R02C01
CD14 cells treated with M-CSF for 5 days in the presence of 50µM cambinol donor 1


title: Li_DFxDF_--_1

description:
procesed data file:
Li_DFxDF_--_1.bw

value: adult liver

tag: genotype  (left position=maternal; right position=paternal)


title: MO_D3

description:
202163550097_R05C01
peripheral blood isolated CD14+ cells (monocytes) donor 3


title: IGR-1_DMSO_8h_rep1


title: Dnmt1 HET rep1


title: Ki_DFxDF_++_4

description:
procesed data file:
Ki_DFxDF_++_4.bw

source_name: adult kidney

value: adult kidney

tag: Sex


title: N724_S511_5 scRNAseq

value: Lymph node


title: N724_S506_5 scRNAseq

value: FACS purified cells


title: Li_DFxDF_--_4

description:
procesed data file:
Li_DFxDF_--_4.bw


title: Dnmt1 HET rep2


title: MO_D2

description:
202163550095_R04C01
peripheral blood isolated CD14+ cells (monocytes) donor 2


title: Adult mouse hippocampus, Control treated with sgLacZ  23

data_processing:
Fastq files were mapped to the mm10 mouse reference genome with the STAR aligner v2.7 (Dobin et al., 2013).
Differential gene expression and Functional enrichment analyses were performed with DESeq2 (Love et al., 2014) and GSEA (Huang et al., 2009), respectively.
Statistical and downstream bioinformatics analyses were performed within the R environment.
Gene expression heatmaps were produced with GENE-E (Broad Institute).
Genome_build: mm10
Supplementary_files_format_and_content: STAR gene counts

source_name: Control treated with sgLacZ

extract_protocol:
RNA was isolated with Trizol (Thermo Fisher), and treated with DNase I (NEB) according to manufacturer's instructions.
Library preparation was done with TruSeq RNA Library Prep Kit v2 (Illumina) according to manufacturer's instructions.

tag: disease state

value: Control

value: sgLacZ

tag: developmental stage

value: adult

value: brain

tag: tissue region

value: hippocampus


title: Adult mouse hippocampus, Control treated with sgLacZ  16


title: Ki_DFxDF_++_2

description:
procesed data file:
Ki_DFxDF_++_2.bw

value: 6 weeks


title: Ki_DFxDF_++_3

description:
procesed data file:
Ki_DFxDF_++_3.bw


title: N724_S503_5 scRNAseq


title: Ki_DFxDF_++_1

description:
procesed data file:
Ki_DFxDF_++_1.bw


title: Adult mouse hippocampus, Control treated with sgLacZ  15


title: Adult mouse hippocampus, Epileptic treated with sgKcna1  11

source_name: Epileptic treated with sgKcna1

value: Epileptic


title: N723_S506_5 scRNAseq


title: Adult mouse hippocampus, Epileptic treated with sgKcna1  10


title: N723_S507_5 scRNAseq


title: Adult mouse hippocampus, Control treated with sgLacZ  14


title: Adult mouse hippocampus, Epileptic treated with sgKcna1  1


title: N727_S505_5 scRNAseq


title: Adult mouse hippocampus, Epileptic treated with sgKcna1  2


title: Ki_DFxDF_--_4

description:
procesed data file:
Ki_DFxDF_--_4.bw


title: Ki_DFxDF_--_3

description:
procesed data file:
Ki_DFxDF_--_3.bw


title: Adult mouse hippocampus, Epileptic treated with sgKcna1  3


title: N723_S505_5 scRNAseq


title: MAC_DMSO_D3

description:
202163550095_R06C01
CD14 cells treated with M-CSF for 5 days in the presence of 0.1 % DMSO donor 3

value: donor 3

value: M-CSF macrophages


title: MAC_DMSO_D1

description:
202163550095_R02C01
CD14 cells treated with M-CSF for 5 days in the presence of 0.1 % DMSO donor 1


title: Adult mouse hippocampus, Epileptic treated with sgKcna1  12


title: Adult mouse hippocampus, Epileptic treated with sgLacZ  9

source_name: Epileptic treated with sgLacZ


title: N723_S503_5 scRNAseq


title: Adult mouse hippocampus, Control treated with sgLacZ  13


title: Ki_DFxDF_--_2

description:
procesed data file:
Ki_DFxDF_--_2.bw

value: F


title: Ki_DFxDF_--_1

description:
procesed data file:
Ki_DFxDF_--_1.bw


title: Adult mouse hippocampus, Epileptic treated with sgLacZ  7


title: N723_S502_5 scRNAseq


title: He_DFxDF_++_4

description:
procesed data file:
He_DFxDF_++_4.bw

source_name: adult heart

value: adult heart


title: Adult mouse hippocampus, Epileptic treated with sgLacZ  6


title: N722_S503_5 scRNAseq


title: N721_S508_5 scRNAseq


title: Adult mouse hippocampus, Epileptic treated with sgLacZ  5


title: Adult mouse hippocampus, Epileptic treated with sgLacZ  4


title: N722_S508_5 scRNAseq


title: KMJR138_DMSO_8h_rep1

value: DMSO


title: He_DFxDF_++_2

description:
procesed data file:
He_DFxDF_++_2.bw


title: He_DFxDF_++_1

description:
procesed data file:
He_DFxDF_++_1.bw


title: He_DFxDF_++_3

description:
procesed data file:
He_DFxDF_++_3.bw


title: N721_S506_5 scRNAseq


title: N721_S507_5 scRNAseq


title: N721_S503_5 scRNAseq


title: He_DFxDF_--_4

description:
procesed data file:
He_DFxDF_--_4.bw


title: Adult mouse hippocampus, Epileptic treated with sgLacZ  8


title: He_DFxDF_--_2

description:
procesed data file:
He_DFxDF_--_2.bw


title: He_DFxDF_--_3

description:
procesed data file:
He_DFxDF_--_3.bw


title: N721_S502_5 scRNAseq


title: N720_S511_5 scRNAseq


title: He_DFxDF_--_1

description:
procesed data file:
He_DFxDF_--_1.bw


title: N720_S510_5 scRNAseq


title: Br_DFxDF_++_4

description:
procesed data file:
Br_DFxDF_++_4.bw

source_name: adult brain

value: adult brain


title: N720_S508_5 scRNAseq


title: Br_DFxDF_++_3

description:
procesed data file:
Br_DFxDF_++_3.bw


title: Br_DFxDF_++_2

description:
procesed data file:
Br_DFxDF_++_2.bw


title: N720_S507_5 scRNAseq


title: Pt 18.6 wt ChipH3K4me3R1

city: Thuwal

first: Alaguraj

last: Veluchamy

address: Thuwal

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

library_source: genomic

data_processing:
Quality check on reads was done using FASTQC
Reads with minimum length of 36 bp was kept after trimming using Trimmomatic.
For peak calling, we used three different peak detection methods such as MUSIC, BCP and MACS2
Genome-wide analysis of tag density profile on TSS (transcriptional start sites) was performed using deeptools
Analysis and Visualization of the data were performed using IGV and R.
Genome_build: Mean and standard deviation of the coverage depth were calculated and plotted using Qualimap and samtools.
Supplementary_files_format_and_content: Peak file in 9 column format. Content is chromosomal co-ordinates.

organism: Phaeodactylum tricornutum

source_name: Whole organism

growth_protocol:
Cells of the reference strain P. tricornutum Pt1 8.6 CCAP 1055/1 (CCMP2561) were harvested after a week of growth in artificial sea water (ref) at 19°C, under 12/12 light dark period with a light intensity of 75 μmol photons m-2 s-1.
cells were grown until around a million cells per ml, at 20 °C , 12h/12 light dark period, at 70 uE/S

extract_protocol:
Normal condition
Library preparation was performed at Fasteris next generation sequencing facilities (Switzerland), using the illumina TruSeq kit and sequencing was run on a HiSeq platform (V4 chemistry) with 1x 50 bp Single-reads.

treatment_protocol: cells were harvested by centrifugation after cross linking with formaldehyde, washed and chromatin was extracted

tag: ecotype

tag: chip antibody

value: H3K4me3, Cell signaling Technology 9751S


title: Pt 18.6 wt ChipH3K4me3R2


title: Pt 18.6 wt Input


title: N720_S505_5 scRNAseq

tag: tissue

tag: passages


title: Camalexin_ctrl_6h_bioRep3

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

institute: INRA

hyb_protocol: The hybridization performed on a NimbleGen Hybridization System 4 (mix mode B) at 42° overnigth. Afterwards, the slide were washed, dried, and scanned.

scan_protocol: Slides were scanned at 532/635nm at 2 μm resolution and high sensitivity with a Roche-NimbleGen MS200. NimbleScan Software v2.4 was used to extract pair-data files from the scanned images.

data_processing: All statistical analyses on the gene expression data were performed using the R language, version 2.5.1 (R Development Core Team, 2011) and the package LIMMA (Smyth G.K., 2005) from the Bioconductor project. For the processing step, data were normalized by the lowess method in LIMMA.

organism: Alternaria brassicicola

label_protocol: 400 ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse-transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1,5mmol of Cyanine-3 (Cy3) or Cyanine-5 (Cy5) (Interchim, France), then purified with NucleoSpin Gel and PCR Clean-up column kits (Macherey-Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND-1000 (Nanodrop Technologies, DE, USA). Labelled samples were combined as 30 pmol for each dye and co-hybridized to the Medtr_v1 12x135K arrays.

growth_protocol: Conidia were first incubated for 24 h on cellophane disks overlaid on solid PDA medium. Germlings and the underlying cellophanes were then taken off from the agar plate and transferred to a second PDA medium for 6h with DMSO

extract_protocol: Total RNA was extracted by using a modified cetyltrimethylammonium bromide method (Verdier et al., 2008)

tag: tissus

value: germlings

tag: genetic background

value: Wild-type

tag: agent

tag: time point

value: 1 day


title: Camalexin_ctrl_6h_bioRep1

tag: genotype


title: Br_DFxDF_++_1

description:
procesed data file:
Br_DFxDF_++_1.bw

tag: strain


title: Brassinin_ctrl_6h_bioRep2

tag: age


title: Brassinin_100_6h_bioRep2

growth_protocol: Conidia were first incubated for 24 h on cellophane disks overlaid on solid PDA medium. Germlings and the underlying cellophanes were then taken off from the agar plate and transferred to a second PDA medium for 6h with brassinin (100 µM)

value: brassinin (100 microM)


title: Brassinin_ctrl_6h_bioRep1


title: Brassinin_ctrl_6h_bioRep3


title: 191696

city: NICE

first: Thibault

last: FABAS

address: 28 av Valombrose

institute: CHU Nice

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Command Console Software (version 3.2.2). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using CHAs (version 4.0). Genomic Smoothing analysis was performed by CHAs
The CNV value is the logarithm base 2 of the sample signal divided by a reference value from the OncoScan_CNV.FFPE.na33.r2.REF_MODEL library. The allelic status is determined accordind the B-Allelic Frequency (BAF = B/(A+B) ; AA : BAF = 0, BB : BAF = 1, AB : BAF = 0,5) or the Allele Difference (Diff = A - B where each A and B allele are 0,5 units. AA : Diff = 1, AB : Diff = 0, BB : Diff = -1)

label: Biotin

source_name: non-polyploid chRCC

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA was extracted from formol fixed-paraffin embedded fragments using Maxwell FFPE DNA LEV Kit (PROMEGA).

value: Chromophobic renal cell carcinomas (chRCC)

tag: ploidy

value: non-polyploid chromophobe rcc

tag: tumor type

value: Eosinophilic variant

tag: pathologic stage


title: Br_DFxDF_--_4

description:
procesed data file:
Br_DFxDF_--_4.bw

tag: background (maternal x paternal for hybrids)

tag: genotype  (left position=maternal; right position=paternal)

tag: Sex


title: 180624


title: Camalexin_50_6h_bioRep1

growth_protocol: Conidia were first incubated for 24 h on cellophane disks overlaid on solid PDA medium. Germlings and the underlying cellophanes were then taken off from the agar plate and transferred to a second PDA medium for 6h with camalexin (50 µM)

value: camalexin (50 microM)


title: N719_S511_5 scRNAseq

value: Lymph node

value: FACS purified cells


title: Brassinin_100_6h_bioRep3


title: Brassinin_100_6h_bioRep1


title: 172455

value: classic histological type


title: Br_DFxDF_--_3

description:
procesed data file:
Br_DFxDF_--_3.bw

value: 6 weeks


title: Camalexin_50_6h_bioRep3


title: Camalexin_ctrl_30min_bioRep3

growth_protocol: Conidia were first incubated for 24 h on cellophane disks overlaid on solid PDA medium. Germlings and the underlying cellophanes were then taken off from the agar plate and transferred to a second PDA medium for 30 min. with DMSO

value: 30 min.


title: Camalexin_50_30min_bioRep3

growth_protocol: Conidia were first incubated for 24 h on cellophane disks overlaid on solid PDA medium. Germlings and the underlying cellophanes were then taken off from the agar plate and transferred to a second PDA medium for 30 min. with camalexin (50 µM)


title: Camalexin_50_6h_bioRep2


title: Camalexin_ctrl_30min_bioRep1


title: Camalexin_ctrl_6h_bioRep2


title: Camalexin_50_30min_bioRep2


title: Camalexin_ctrl_30min_bioRep2


title: Br_DFxDF_--_2

description:
procesed data file:
Br_DFxDF_--_2.bw

value: F


title: N719_S510_5 scRNAseq


title: 162750


title: Br_DFxDF_--_1

description:
procesed data file:
Br_DFxDF_--_1.bw


title: Brassinin_ctrl_30min_bioRep3

value: DMSO


title: 192077


title: N719_S502_5 scRNAseq


title: Camalexin_50_30min_bioRep1


title: N718_S511_5 scRNAseq


title: Ctrl10

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

description: Sample 25

data_processing:
Basecalls and demultiplexing was performed using CASAVA version 1.8.3 for samples labeled 7-10 and OLB version 1.9.4 for samples labeled 1-6
RNA-seq reads were aligned to the mm9 genome assembly using STAR version 2.1.4a with the default parameters:  STAR --genomeDir mm9.fasta --readFilesIn $end1 $end2 --runThreadN 8
Uniquely aligned reads were quantified against the Refseq annotation mm9.gtf using HTSeq with the following parameters: htseq-count -m intersection-nonempty -s 'no' - mm9.gtf
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file including RPKM  abundance measurements for each Sample

source_name: Oligodendrocyte Precursor Cells

extract_protocol:
Mouse brain LCM samples had cDNA ampified by Nugen RNAseq Ovation kit
RNA libraries were prepared for sequencing using Illumina TruSeq with Nugen Library to be prepared for multiplex Hiseq runs from the provided samples. 100 bp two-paired end, 3 samples to be run per lane. Barcode information is listed in each sample fastq read id and one unique tag is used per sample.

tag: condition

value: Control


title: 163302


title: N718_S510_5 scRNAseq


title: 192078


title: Ctrl8

description: Sample 23


title: N718_S508_5 scRNAseq


title: N720_S503_5 scRNAseq


title: 150098

source_name: polyploid chRCC

value: polyploid chromophobe rcc


title: Ctrl7

description: Sample 22


title: N718_S507_5 scRNAseq


title: 162566


title: N718_S506_5 scRNAseq


title: Ctrl5

description: Sample 20


title: 150340

value: hybrid oncocytic/chromophobe tumours  variant


title: Brassinin_100_30min_bioRep3

growth_protocol: Conidia were first incubated for 24 h on cellophane disks overlaid on solid PDA medium. Germlings and the underlying cellophanes were then taken off from the agar plate and transferred to a second PDA medium for 30 min. with brassinin (100 µM)

value: germlings

value: Wild-type


title: N718_S503_5 scRNAseq


title: Brassinin_ctrl_30min_bioRep1

value: 1 day


title: 171859

value: Chromophobic renal cell carcinomas (chRCC)


title: Ctrl9

description: Sample 24


title: 173365


title: N719_S503_5 scRNAseq


title: N716_S508_5 scRNAseq


title: Ctrl6

description: Sample 21


title: Naive_1

city: Atlanta

first: Haydn

last: Kissick

state: Georgia

address: 1462 Clifton Rd

institute: Emory University

data_processing:
Rna samples: Adapter trim with cutadapt, align with StarAligner, counts with Htseqcount, differential expression between groups with DESeq2
DNA methylation: Adapter trim with cutadapt, differentially methylated CpGs identified by fisher exact test compared to each CpGs Naïve cells, Differentially methylated regions identified using custom python analysis finding continuous regions with atleast 5/10 significantly (p=0.0001) differentially methylated CpGs
Genome_build: hg38
Supplementary_files_format_and_content: Counts

source_name: Naive

extract_protocol:
RNA and DNA was extracted using qiagen all-prep kits
DNA methylation was done using illumina methylseq protocol, Bladder rna libraries  were prepared using Nugen Ovation, Kidney and prostate RNA libraries prepared using clontech smartseq V2

value: Blood

tag: cell type

value: CD8 T-cell

tag: cell subtype


title: Ctrl3

description: Sample 18


title: Ctrl4

description: Sample 19


title: Brassinin_100_30min_bioRep1

value: brassinin (100 microM)


title: Camalexin_50_2h_bioRep2

growth_protocol: Conidia were first incubated for 24 h on cellophane disks overlaid on solid PDA medium. Germlings and the underlying cellophanes were then taken off from the agar plate and transferred to a second PDA medium for 2h with camalexin (50 µM)

value: camalexin (50 microM)


title: Camalexin_ctrl_2h_bioRep3

growth_protocol: Conidia were first incubated for 24 h on cellophane disks overlaid on solid PDA medium. Germlings and the underlying cellophanes were then taken off from the agar plate and transferred to a second PDA medium for 2h with DMSO


title: Camalexin_ctrl_2h_bioRep2


title: Ctrl1

description: Sample 16


title: Camalexin_ctrl_2h_bioRep1


title: Kidney_stem_1

tag: tissue

value: Kidney tumor


title: Camalexin_50_2h_bioRep1

tag: tissus


title: N718_S502_3 scRNAseq

value: Lymph node

tag: passages

value: FACS purified cells


title: N716_S506_5 scRNAseq


title: N716_S502_3 scRNAseq


title: N719_S502_3 scRNAseq


title: Kidney_ef_2


title: Kidney_ef_1


title: Ctrl2

description: Sample 17


title: 5d10

description: Sample 15

value: white matter stroke

value: Day 5


title: 5d8

description: Sample 13


title: Kidney_stem_2


title: Camalexin_50_2h_bioRep3

tag: genetic background

tag: agent


title: IPSC_D14_C

city: Aurora

first: Edward

last: Lau

state: CO

address: 12700 E19th Av RCII Rm 8004

department: Medicine/Cardiology

institute: University of Colorado

description: IPSC, DR20

data_processing:
Reads were aligned to reference genome using STAR v.2.5.0a with —sjdbOverhang 149 and default parameters
Aligned reads were assembled into genes and transcripts and quantified using stringtie v.1.3.5  with -e
Genome_build: GRCh38
Supplementary_files_format_and_content: comma-separated values containing gene count or transcript count in each sample

source_name: Induced pluripotent stem cell-derived

growth_protocol: Human induced pluripotent stem cells were acquired from cryopreserved stocks in the Stanford Cardiovascular Institute Biobank and expanded in monolayer in Gibco E8 medium on Matrigel matrix.

extract_protocol:
Total cellular RNA were extracted by 300 µL TRIzol/chloroform per 10e6 cells, followed by solid-phase extraction using QIAgen RNeasy mini columns.
RNA-seq library was prepared using standard Illumina protocol with oligo(dT) bead enrichment for mRNA.

treatment_protocol: Cells were directed to differentiate into cardiomyocytes using published methods (Burridge et al. Nat Methods 2014); briefly, cells at 90% confluence in 6-well-plates were treated with 6 µM CHIR-99021 in RPMI-1640 with B27 for 2 days to induce mesoderm specification, allowed to recover for 1 day, then treated with 5 µM IWR-1-endo for 2 days for cardiac specification. On day 7, culture medium was changed to RPMI-B27 with insulin. Cells were glucose-starved on day 10 to day 14.

tag: time point

value: 14 days

tag: cell stage

value: cardiomyocyte

tag: source

value: SCVI


title: IPSC_D14_B

description: IPSC, DR20


title: 5d9

description: Sample 14

tag: age


title: Brassinin_ctrl_30min_bioRep2

tag: genotype

value: DMSO

value: 30 min.


title: B_Stem_4

value: Bladder tumor


title: 5d7

description: Sample 12


title: IPSC_D14_A

description: IPSC, DR20


title: Brassinin_100_30min_bioRep2

value: germlings

value: Wild-type

value: 1 day


title: 5d6

description: Sample 11


title: Brassinin_100_2h_bioRep2

growth_protocol: Conidia were first incubated for 24 h on cellophane disks overlaid on solid PDA medium. Germlings and the underlying cellophanes were then taken off from the agar plate and transferred to a second PDA medium for 2h with brassinin (100 µM)


title: B_Stem_3

value: CD8 T-cell


title: Brassinin_100_2h_bioRep3

value: brassinin (100 microM)


title: Brassinin_ctrl_2h_bioRep1


title: Brassinin_100_2h_bioRep1


title: 5d4

description: Sample 10


title: IPSC_D7_B

description: IPSC, DR24

value: 7 days

value: early cardiomyocyte


title: B_Stem_2


title: IPSC_D7_A

description: IPSC, DR24


title: B_Ef_2


title: 5d3

description: Sample 9


title: B_Stem_1


title: 15d9

description: Sample 7

value: Day 15


title: 5d1

description: Sample 8


title: IPSC_D7_C

description: IPSC, DR24


title: B_Ef_1


title: IPSC_D2_B

description: IPSC, DR19

value: 2 days

value: mesoderm


title: IPSC_D2_C

description: IPSC, DR19


title: 15d8

description: Sample 6

value: white matter stroke


title: HNCC-BSY

city: Hangzhou

first: Wenbiao

last: Chen

address: Zhejiang University, Hangzhou

country: China

institute: Zhejiang University

hyb_protocol: Agilent surehyb is used for hybridization experiments

scan_protocol: Agilent DNA microarray scanner was used for scanning, agilent feature extraction software (v11.0.1.1) was used to collect chip probe signal value, and agilent genespring software was used for chip standardization

data_processing:
Agilent genespring GX V12.2 software was used to select differentially expressed lncRNA and mNRA, and the differentially expressed mrnas were analyzed by GO and KEGG
Differentially expressed lncRNAs and mRNAs with statistical significance between two groups were identified through  plot filtering with a threshold of fold-change (test/control)>2 and P<0.05

source_name: hepatocellular carcinoma

label_protocol: Arraystar RNA flash labeling kit is used for labeling samples

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: The tumor was removed surgically in patients with liver cancer

value: hepatocellular carcinoma

tag: hbv status

value: no HBV-related Hepatocellular carcinoma


title: mx0019

city: St. Louis

first: Brian

last: Kim

state: MO

address: 660 S Euclid Ave

institute: Washington University in Stl

data_processing:
Sequences were aligned with STAR v2.0.4b
Gene counts were determined with Subread:featureCount v1.4.5
Transcript abundance was determined with Sailfish v0.6.3
Sequence performace was assessed with RSeQC v2.3
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data files are the counts tables from Subread:featureCount for each sample as a text file

source_name: skin

extract_protocol:
4 mm skin biopsies of skin from atopic dermatitis patients or deidentified healthy margin surgical tissue were obtained; skin samples were placed in RNA Later and tissue was lysed using a bead homogenizer followed by RNA isolation using the RNeasy mini kit (QIAGEN)
rRNA was depleted using RiboZERO kit (Illumina), mRNA was fragmented in buffer containing 40 mM Tris acetate (pH 8.2), 100 mM potassium acetate, and 30 mM magnesium acetate and heated to 94C for 150 s. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Invitrogen, per manufacturer’s instructions) and random hexamers. A second strand reaction was performed to yield dscDNA. cDNA was blunt ended, had an A base added to the 30 ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12 cycles using primers incorporating unique index tags. Fragments were sequenced on an Illumina HiSeq-3000 using single reads extending 50 bases.

value: skin

value: healthy margin


title: Brassinin_ctrl_2h_bioRep3

value: DMSO


title: Brassinin_100_20h_bioRep2

growth_protocol: Conidia were first incubated for 24 h on cellophane disks overlaid on solid PDA medium. Germlings and the underlying cellophanes were then taken off from the agar plate and transferred to a second PDA medium for 20h with brassinin (100 µM)


title: Brassinin_ctrl_20h_bioRep2

growth_protocol: Conidia were first incubated for 24 h on cellophane disks overlaid on solid PDA medium. Germlings and the underlying cellophanes were then taken off from the agar plate and transferred to a second PDA medium for 20h with DMSO


title: Brassinin_100_20h_bioRep1


title: mx0018


title: Brassinin_ctrl_20h_bioRep1


title: 15d5

description: Sample 3


title: IPSC_D2_A

description: IPSC, DR19

value: SCVI


title: ad017

value: atopic dermatitis


title: IPSC_D0_C

description: IPSC, DR15

value: 0 day

value: pluripotent


title: 15d6

description: Sample 4


title: mx0014


title: IPSC_D0_A

description: IPSC, DR15


title: mx0007


title: Naive_2

value: Blood

value: CD8 T-cell


title: 15d3

description: Sample 2


title: LPS_BR2

city: Tezpur

first: Rupak

last: Mukhopadhyay

state: - If in U.S, Select a State -

address: Napaam, Sonitpur, Assam

department: Department of Molecular Biology and Biotechnology

institute: Tezpur University

description: Gene expression after 2 hours treatment

hyb_protocol: Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Scanned using the Agilent Microarray Scanner

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift. Gene based analysis was performed.

source_name: THP-1 macrophage

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: THP1 monocytic cells were maintained in liquid RPMI-1640 media supplemented with 2 mM glutamine, 10% heat inactivated fetal-bovine serum BS and penicillin/streptomycin (100 units/ml, 100 µg/ml), at 37°C in 5% CO2

extract_protocol: RNA was prepared using the Qiagen RNeasy mini kit (Qiagen GmbH, Hilden) following the manufacturer's recommendations. RNA was quantified using NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: THP1 monocytes were differentiated to macrophage like cells with 5 mg/ml of phorbol myristed 13-acetate (PMA) for 48 hours.PMA containing media was discarded and washed with Dulbecco's PBS twice and kept for another 6 hours in complete RPMI-1640 media. THP-1 macropahegs were either treated with TNFα, IL-6, LPS or PBS for 2 hours. After treatment, cells were harvested in RNAlater (Ambion).

tag: treatment

value: LPS

value: Monocyte/macrophage

tag: cell line


title: HNCC-HJD


title: HNCC-BSG


title: HNCC-SQX


title: HNCC-WTZ


title: ad013


title: LPS_BR1

description: Gene expression after 2 hours treatment


title: 15d7

description: Sample 5

value: Day 15


title: HNCC-CFL


title: 15d2

description: Sample 1


title: HNCC-ZGX


title: ad016


title: IPSC_D0_B

description: IPSC, DR15


title: ad014


title: IL-6_BR2

description: Gene expression after 2 hours treatment


title: ModM3 OFF3

city: Gold Coast

first: Kate

last: Seib

state: QLD

address: Parklands Drive

department: Institute for Glycomics

institute: Griffith University

data_processing:
The primary sequence data was generated using the Illumina bcl2fastq 2.20.0.422 pipeline.
STAR aligner v2.5.3a was used to map reads to the reference genome sequence.
Transcripts were assembled with Stringtie v1.3.3 utilising the reads alignment and reference annotation based assembly option (RABT).
Differential expression analysis was performed with edgeR version 3.22.3.
Genome_build: ASM208012v1
Supplementary_files_format_and_content: raw read counts and differential expression analysis. Full gene name is included in the file OFF.VS.ON-all_genes.txt

organism: Moraxella catarrhalis

source_name: Bacteria

growth_protocol: Moraxella catarrhalis strains 195ME ModM3 ON and OFF were cultured in triplicate on BHI agar at 37 °C with 5% CO2 overnight (16 hours). Each strain was then re-suspended in 20 mL BHI broth to an optical density of OD600 = 0.05 and grown for a further 3 hours at 37°C with orbital shaking at 200rpm.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) and residual DNA digested using RNase-Free DNase Set (Qiagen) as per manufacturer’s instructions.
RNA libraries were prepared using the Illumina Ribo-Zero Gold protocol. Pooling and clustering of libraries was performed using the Illumina cBot system with TruSeq PE Cluster kit v3 reagents.

treatment_protocol: 2 mL of culture was added directly to 4 mL of RNAprotect Bacteria Reagent (Qiagen), and incubated at room temperature for 5 minutes. Cultures were pelleted by centrifugation at 5,000 x g for 10 minutes at 4°C and the supernatant was discarded. Pellets were resuspended in 200 µL of lysis buffer (30 mM Tris·Cl, 1 mM EDTA, pH 8.0) containing 15 mg/mL lysozyme and 80 units/mL proteinase K.

tag: strain


title: ModM3 OFF2


title: HBCC-WRT

value: HBV-related Hepatocellular carcinoma


title: ModM3 OFF1


title: ModM3 ON2


title: Control_BR2

description: Gene expression after 2 hours treatment

value: control


title: HBCC-WYG


title: IL-6_BR1

description: Gene expression after 2 hours treatment


title: TNFα_BR1

description: Gene expression after 2 hours treatment

value: TNFα


title: pXEN-like-3

city: Harbin

first: Yan

last: Li

address: ,600 Changjiang Road,Xiangfang District

institute: Northeast Agriculture University

data_processing:
Smart-Seq2 method was used to amplify the single cell sample. The reaction system for the first cDNA strand synthesis comprised the reverse transcription enzyme, buffer, TSO primers and oligo-dT primers with common sequence. For the second strand synthesis, added PCR amplification reagent and ISPCR primer with common sequence to the first strand products. The sample cDNA was fragmented into 300bp by Bioruptor®Sonication System (Diagenode Inc.), and then performed terminal repair, addition of A, and ligation of sequencing adapters, and amplified. The PCR amplification product with 350-450bp was extracted. Then, the concentration was measured by Qubit 2.0 Flurometer (Life Technologies, CA, USA). The integrity of the amplified products was detected by Agilent 2100 High Sensitivity DNA Assay Kit (Agilent Technologies, CA, USA). The libraries were sequenced by an Illumina HiSeq X Ten platform.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Sus scrofa

source_name: pig embryo

growth_protocol: Using a serum-free culture system, we directly derived porcine extraembryonic endoderm like cells (pXEN-like cells) fom day 6-7 blastocysts ,The piPSCswas cultured in pEPSCM medium

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: type

value: Extraembryonic endoderm stem cells


title: piPSCs-3

source_name: porcine fetal fibroblasts

value: Induced pluripotent stem cells


title: TNFα_BR2

description: Gene expression after 2 hours treatment

tag: cell type


title: piPSCs-2


title: HBCC-WZX

value: hepatocellular carcinoma


title: High glutamine incubation (10 mM) in human in vitro differentiated adipocyte_rep 3

first: Simon

last: Lecoutre

address: Huddinge

department: MedH

description:
High_Glutamine _3
Gene expression data of human in vitro differentiated adipocyte day 11 treated with 10 mM of glutamine during differentiation.

hyb_protocol: Hybridization, washing and staining were carried out on Clariom D Human arrays, using Affymetrix GeneChip Fluidics Station 450 according to the manufacturer’s protocol.

scan_protocol: The fluorescent intensities were determined with Affymetrix GeneChip Scanner 3000 7G, and Affymetrix GeneChip Command Console (AGCC, v.4.1.2) was used to analyze the acquired array images.

data_processing:
Gene-level SST-RMA processing and sample group comparisons were performed using Transcriptome Analysis Console (TAC, v.4.0).
Nominally significant genes (p<0.01) were analysed in a gene ontology (GO) analysis performed using an online web tool (https://david.ncifcrf.gov/).

label_protocol: Biotinylated DNA targets was prepared from 150 ng total RNA using the GeneChip WT Plus Reagent Kit according to the manufacturer's instructions.

growth_protocol: Cultures of in vitro differentiated human adipocytes were set up and differentiated in media containing a standard differentiation adipogenic cocktail; 5 mg/ml insulin, 0.25 mmol/l dexamethasone, 0.5 mmol/l 3-isobutyl-1-methylxanthine (IBMX) and 10 mmol/l rosiglitazone for two days after which the dexamethasone and IBMX were removed and the cells were allowed to undergo full adipogenic differentiation.

extract_protocol: Total RNA was extracted from human in vitro differentiated adipocyte. RNA quantity was measured using NanoDrop ND-1000 Spectrophotometer.

treatment_protocol: Human in vitro differentiated adipocyte day 13 treated with siSP1 or siC at day 9 (SP1-regulated transcriptome) or human in vitro differentiated adipocyte day 11 treated with 0.5 mM (L) or 10 mM (H) of glutamine during differentiation.

value: in vitro differentiated adipocyte

value: High glutamine


title: High glutamine incubation (10 mM) in human in vitro differentiated adipocyte_rep 2

description:
High_Glutamine _2
Gene expression data of human in vitro differentiated adipocyte day 11 treated with 10 mM of glutamine during differentiation.


title: HBCC-LJG


title: HBCC-GHZ


title: High glutamine incubation (10 mM) in human in vitro differentiated adipocyte_rep 1

description:
High_Glutamine _1
Gene expression data of human in vitro differentiated adipocyte day 11 treated with 10 mM of glutamine during differentiation.


title: HBCC-CZL


title: ModM3 ON3


title: pXEN-like-2


title: ModM3 ON1


title: pXEN-like-1


title: Secretory-stage, biological rep 5

first: Michael

last: Paine

address: 2250 Alcazar Street

institute: USC

description: Gene expression of maturation-stage enamel organ from rat incisor

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 15 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

organism: Rattus norvegicus

source_name: Maturation-stage enamel organ from rat incisor

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was prepared using miRNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer`s recommendations

value: Maturation-stage enamel organ

value: Wistar Hannover


title: Low glutamine incubation (0.5 mM) in human in vitro differentiated adipocyte_rep 3

institute: Karolinska Institutet

description:
Low_Glutamine _3
Gene expression data of human in vitro differentiated adipocyte day 11 treated with 0.5 mM of glutamine during differentiation.

value: Low glutamine


title: HBCC-JAP


title: Maturation-stage, biological rep 5

description: Gene expression of secretory-stage enamel organ from rat incisor

source_name: Secretory-stage enamel organ of rat incisor

value: Secretory-stage enamel organ


title: Maturation-stage, biological rep 4


title: Cervical loop, biological rep 5

description: Gene expression of cervical loop enamel organ from rat incisor

source_name: Cervical loop enamel organ from rat incisor

value: Cervical loop enamel organ


title: Control_BR1

description: Gene expression after 2 hours treatment


title: TRAP Sm Rep#2

city: La Plata

first: Soledad

last: Traubenik

state: Buenos Aires

department: Ciencias Biologicas

country: Argentina

institute: Universidad Nacional de La Plata

description: polyA RNA from TRAP RNA purified with oligodT-magnetic beads

data_processing:
Illumina Casava1.7 software used for basecalling.
Illumina reads were aligned to the M. truncatula genome (Mtv4.0) using Tophat 2 (Kim et al., 2013).
Transcript assembling  and Fragments Per Kilobase of exon per Megabase of library size (FPKM)  counts were performed using Cufflinks
Supplementary_files_format_and_content: FPKM

organism: Medicago truncatula

source_name: roots

growth_protocol: Transgenic roots were generated by Agrobacterium rhizogenes-mediated transformation as previously described (Boisson-Dernier et al., 2001). Plants that developed hairy roots were transferred to slanted boxes containing Fahraeus media free of nitrogen. Seedlings were grown at 25°C with a long-day period (16-h day/8-h night cycle) and 50% humidity. Roots were inoculated with 10 ml of a 1:1000 dilution of S. meliloti 1021 (Meade and Signer, 1977) culture grown in liquid TY media until OD600 reached 0.8 or with 10 ml of water as a control (mock treatment).

extract_protocol:
RNA was extracted with Trizol
Illumina Truseq RNA Sample Prepv2

treatment_protocol: Roots grown on agar-fahreaus plates were inoculated with water or a suspension of Sinorhizobium meliloti

value: Roots inoculated with S. meliloti 1021

tag: sample type

value: TRAP RNA

tag: transformation

value: Hairy roots transformed with p35S:HFMtRPL18


title: TRAP Sm Rep#1


title: Cervical loop, biological rep 4

tag: tissue


title: Maturation-stage, biological rep 3


title: TRAP mock Rep#2

value: Roots inoculated with water


title: TRAP mock Rep#1


title: Total Sm Rep#2

description: polyA RNA from Total cellular RNA purified with oligodT-magnetic beads

value: Total Cellular RNA


title: Low glutamine incubation (0.5 mM) in human in vitro differentiated adipocyte_rep 2

city: Stockholm

description:
Low_Glutamine _2
Gene expression data of human in vitro differentiated adipocyte day 11 treated with 0.5 mM of glutamine during differentiation.


title: Secretory-stage, biological rep 4


title: Salivary gland_14 day resected_ replicate 3

city: Albany

first: Melinda

last: Larsen

address: 1400 Washington Ave., LSRB 10

department: Dept. of Biological Science

institute: University at Albany, SUNY

hyb_protocol: Following fragmentation, 3.5 ug of cRNA were hybridized for 16 hr at 45C on Clariom S mouse Array. GeneChips were washed and stained on a GeneChip 3000 7G scanner using Affymetrix GeneChip Command Console Software (AGCC).

scan_protocol: GeneChips were scanned using GeneChip 3000 7G scanner.

data_processing: Data analysis was performed using Transcriptome Analysis Console (TAC 4.0) Software, Applied Biosystems. CEL files were quantile-normalized with Gene Level- RMA and differential analysis was done using ANOVA with a Benjamini Hochberg False Discovery Rate correction (p<0.05) and a fold change filter of 2.

source_name: Day 14 Resected salivary gland

label_protocol: Biotinylated cRNA were prepared from 100ng total RNA according to the standard Affymetrix WT Plus protocol

growth_protocol: Mice were bred and raised in a normal 12 hour light/dark cycle in the University at Albany, SUNY Laboratory Animal Research facility.

extract_protocol: Total RNA was isolated using TRIzol/chloroform following manufacturer's protocol with the following modifications: one additional chloroform step after aqeous layer isolation, RNA was precipitated using 2 volumes 100% molecular grade ethanol and 1/10 volume sodium acetate (ph=5.2) and incubated at -80C for 2 hours, and one additional ethanol wash was added to the wash steps prior to air drying the pellet.

treatment_protocol: Mice underwent either partial salivary gland resection or mock surgery treatment and were allowed to heal for 3 or 14 days.  Mock surgery mice were only allowed to heal for 3 days.

value: salivary gland

tag: gender

value: female

tag: treament

value: partial salivary gland resection; allowed to heal 14 days


title: Cervical loop, biological rep 3


title: MAC_Camb_D3

first: Esteban

last: Ballestar

institute: Josep Carreras Research Institute (IJC)

description: CD14 cells treated with M-CSF for 5 days in the presence of 50µM cambinol donor 3

hyb_protocol: Hybridization was performed using GeneChip® High Throughput Pico Kit (Affymatrix) according to manufacturers' instructions

scan_protocol: Scanning was performed using GeneChip® High Throughput Pico Kit (Affymatrix) according to manufacturers' instructions

data_processing: Raw data were process using the R language. First, background normalisation was performed using Robust Microarray Analysis (RMA) normalisation provided by oligo package. Each probe was then annotated using clariomshumantranscriptcluster.db package, and the average expression level was calculated if more than one probe was mapped to the same gene.

label_protocol: Labelling was performed using GeneChip® High Throughput Pico Kit (Affymatrix) according to manufacturers' instructions

growth_protocol: Monocytes were isolated from buffy coats by CD14 positive selection (MACS) and differentiated with the addition of 25 ng/ml of human M-CSF (PeproTech) for 5 days in the presence of 0.1 % DMSO or 50 µM cambinol

extract_protocol: Total RNA was isolated utilising Maxwell® RSC simplyRNA Cells Kit (Promega)

tag: donor

value: donor 3

value: M-CSF macrophages

value: cambinol


title: Low glutamine incubation (0.5 mM) in human in vitro differentiated adipocyte_rep 1

description:
Low_Glutamine _1
Gene expression data of human in vitro differentiated adipocyte day 11 treated with 0.5 mM of glutamine during differentiation.

value: in vitro differentiated adipocyte


title: Cervical loop, biological rep 2


title: Salivary gland_14 day resected_ replicate 1


title: MAC_DMSO_D2

description: CD14 cells treated with M-CSF for 5 days in the presence of 0.1 % DMSO donor 2

value: donor 2

value: DMSO


title: Salivary gland_14 day resected_ replicate 2


title: MO_D2

description: peripheral blood isolated CD14+ cells (monocytes) donor 2

value: Monocytes


title: MAC_DMSO_D3

description: CD14 cells treated with M-CSF for 5 days in the presence of 0.1 % DMSO donor 3


title: Salivary gland_3 day resected_ replicate 2

source_name: Day 3 Resected salivary gland

value: partial salivary gland resection; allowed to heal 3 days


title: Salivary gland_3 day resected_ replicate 1


title: Maturation-stage, biological rep 2

value: Secretory-stage enamel organ

value: Wistar Hannover


title: Salivary gland_3 day resected_ replicate 3


title: MAC_Camb_D1

description: CD14 cells treated with M-CSF for 5 days in the presence of 50µM cambinol donor 1

value: donor 1


title: Secretory-stage, biological rep 1


title: Total mock Rep#2

value: Hairy roots transformed with p35S:HFMtRPL18


title: Secretory-stage, biological rep 3

value: Maturation-stage enamel organ


title: MO_D3

description: peripheral blood isolated CD14+ cells (monocytes) donor 3


title: MAC_Camb_D2

description: CD14 cells treated with M-CSF for 5 days in the presence of 50µM cambinol donor 2


title: Maturation-stage, biological rep 1


title: MAC_DMSO_D1

description: CD14 cells treated with M-CSF for 5 days in the presence of 0.1 % DMSO donor 1


title: Total mock Rep#1

description: polyA from Total cellular RNA purified with oligodT-magnetic beads

value: Roots inoculated with water

value: Total Cellular RNA


title: piPSCs-1

value: Induced pluripotent stem cells

tag: passages


title: Secretory-stage, biological rep 2

description: Gene expression of maturation-stage enamel organ from rat incisor


title: Total Sm Rep#1

value: Roots inoculated with S. meliloti 1021


title: Salivary gland_mock 3 day_ replicate 3

source_name: Day 3 Mock salivary gland

value: salivary gland

value: female

value: mock surgery


title: Brassinin_ctrl_2h_bioRep2

tag: tissus

value: germlings

tag: genetic background

value: Wild-type

tag: agent

tag: time point

value: 1 day


title: islet_ATAC-Seq_rep4

status: Public on Nov 14 2019

city: La Jolla

first: Maike

last: Sander

address: 2880 Torrey Pines Scenic Dr.

institute: UC San Diego

description: ATAC-seq of islet cells-replicate 4

data_processing:
adaptors were trimmed from ATAC-Seq reads using the trim_galore package
reads were mapped to human reference genome hg19 using bwa
mapped reads were filtered by Samtools, skip alignment with MAPQ smaller than 30, remove duplicate reads, remove mitochondrial reads
peaks were called using mac2, with the parameters: --nomodel --shift -100 --extsize 200 -B --broad --keep-dup all --nolambda
Genome_build: hg19
Supplementary_files_format_and_content: peak file in bed format

source_name: human cadaveric islet

growth_protocol: Human cadaveric islet cells were directly isolated from donors.

extract_protocol:
Roughly 50,000 islet cells were used for each ATAC-Seq assay following the protocol described in Buenrostro et al. (2013). Briefly, cell nuclei was isolated using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630).
The nuclei pellet was resuspended in the transposase reaction mix; 25 μL 2× TD buffer, 2.5 μL transposase (Illumina) and 22.5 μL nuclease-free water at 37°C for 30 min. Then transposed DNA fragments were purified using the Qiagen MinElute kit and amplified 10-12 cycles using the Nextera (Illumina) PCR primers. Libraries were sequenced on HiSeq4000 platform.

treatment_protocol: Human cadaveric islet cells were collected and then genomic DNA was extracted to proceeded to ATAC-seq library preparation.

value: a mixture of alpha, beta, delta, PP cells

value: fully differentiated

value: endocrine tissue


title: islet_ATAC-Seq_rep2

description: ATAC-seq of islet cells-replicate 2


title: islet_ATAC-Seq_rep5

description: ATAC-seq of islet cells-replicate 5


title: islet_ATAC-Seq_rep3

description: ATAC-seq of islet cells-replicate 3


title: Cervical loop, biological rep 1

tag: age

value: Cervical loop enamel organ

value: Wistar Hannover


title: islet_ATAC-Seq_rep1

description: ATAC-seq of islet cells-replicate 1


title: HepG2_model2

first: li

last: lei

address: xiashas street num 6

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Insulin induction

growth_protocol: HepG2 cells (Cell Bank of the Chinese Academy of Sciences, Shanghai, China) were cultured in 1640 medium (Hyclone, Beijing, China) containing 10% fetal bovine serum (FBS, Hyclone, Beijing, China) and 1 × streptomycin in a 37 ℃ 5% CO2 saturated humidity incubator. The normally cultured HepG2 cell lines in log phase were centrifuged at 100grpm for 5 min, and 20000 cells/well were placed in a 96-well plate and incubated at 37°C.The experiment was performed in 24-h control group, 24-h model group, 36-h control group, 36-h model group, 48-h control group, 48-h model group, 72-h control group and 72-h model group.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was used to deplete ribosomal RNA according to the manuscript of the Epicentre Ribo-Zero Gold Kit (Illumina, San Diego, USA). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (LC Bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Insulin (Gibco, NY, USA) was diluted to a final concentration of 10-6 mol/L in complete medium. 200µl insulin preparation was added into each well for the model group and an equal amount of complete medium was added into each well for the control group. Culture was performed in a 37 ℃ 5% CO2 and saturated humidity incubator.


title: HepG2_control1


title: HepG2_APBBR2

source_name: Insulin induction and APBBR treatment


title: HepG2_model3


title: MO_D1

city: Badalona, Barcelona

address: Ctra de Can Ruti, Camí de les Escoles s/n

description: peripheral blood isolated CD14+ cells (monocytes) donor 1

value: donor 1

value: Monocytes


title: HepG2_model1


title: HepG2_control2


title: HepG2_APBBR3


title: Salivary gland_mock 3 day_ replicate 2


title: Salivary gland_mock 3 day_ replicate 1


title: HepG2_APBBR1


title: BMPR2 ∆E2 rep3

city: Berlin

first: Petra

last: Knaus

state: Berlin

address: Thielallee 63

department: Department of  Chemistry and Biochemistry

institute: Freie Universität Berlin

data_processing:
Single-end, 75 bp reads from Illumina sequencing were mapped to the reference genome (hg19) using the STAR mapper (splice junctions based on RefSeq; options: ‐‐alignIntronMin20 ‐‐alignIntronMax500000 ‐‐outFilterMismatchNmax 10). Differential gene expression was ascertained using the DESeq2 package.
Genome_build: hg19
Supplementary_files_format_and_content: excel sheet including RPKM values for each Sample

source_name: EAhy926 cells

growth_protocol: 50.000 EAhy926 cells were seeded  in a 12 well for 3 days in M199 medium (Sigma-Aldrich) supplemented with 20% fetal calf serum (FCS) (Biochrom, Germany), 2mM L-glutamine (PAN-Biotech, Germany), 100 units/ml penicillin, 10µg/ml streptomycin (PAA-laboratories), 25µg/ml Heparin (Sigma-Aldrich) and 50µg/ml endothelial cell growth supplement (Corning, NY, USA), at 37°C and 5% CO2 atmosphere.

extract_protocol:
total RNA was isolated from cells three days after seeding using NucleoSpin® RNA kit from MACHEREY-NAGEL.
After initial quality control using Agilent’s Bioanalyzer, sequencing libraries were prepared from 500ng of total RNA per sample following Roche’s stranded “KAPA RNA HyperPrep” library preparation protocol for single indexed Illumina libraries: First the polyA-RNA fraction was enriched using oligo-dT-probed paramagnetic beads. Enriched RNA was heat-fragmented and subjected to first strand synthesis using random priming. The second strand was synthesized incorporating dUTP instead of dTTP to preserve strand information. After A-tailing Illumina sequencing compatible adapters were ligated. Following bead-based clean-up steps the libraries were amplified using 10 cycles of PCR. Library quality and size was checked with qBit, Agilent Bioanalyzer and qPCR. Sequencing was carried out in biological triplicates on an Illumina HiSeq 4000 system in SR75bp mode (single read, 75 bp read length) yielding between 46-69 million fragments per sample.

treatment_protocol: WT and BMPR2 mutant cells were grown as confluent monolayer in full medium conditions for 3 days without medium change.

value: Endothelial cells

tag: genotype


title: BMPR2 KO rep1

tag: cell line


title: BMPR2 KO rep3


title: BMPR2 KO rep2


title: BMPR2 ∆E2 rep1


title: BMPR2 wt rep3


title: BMPR2 ∆E2 rep2


title: HepG2_control3


title: BMPR2 wt rep1


title: Hs_H1_WT_D8-10-mIR127_RNAseq_1

description:
RNA-seq of PP cells transduced with miR-127 at day8 and harvested at day10
mir127_FPKM_log2_nozeros.txt

data_processing:
Reads were aligned to the hg19 by STAR with parameters: --outSAMstrandField intronMotif --outFilterMultimapNmax 1 --runThreadN 5.Only the reads aligned uniquely to one genomic location were retained for subsequent analysis.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: gene expression data table in text format

source_name: Pancreatic progenitor cells

growth_protocol: Pancreatic progenitor stage cells were cultured in stage 4 medium (MCDB 131 medium, 2.5 g/L NaHCO3, 1X GlutaMAX, 10 mM D-glucose, 2% BSA) and supplemented with 0.25 mM L-Ascorbic Acid (VIT-C), 2 ng/mL FGF7, 0.25 µM SANT-1, 0.1 µM Retinoic Acid, 200 nM LDN193189, 1:200 ITS-X, 100nM TPB and incubated at 37˚C and 5% CO2.

extract_protocol:
mRNA was extracted using miReasy mini kit from Qiagen.
Libraries were prepared using the protocol from Dr. Sander lab. Briefly, RNA were first poly A selected and then subject to RNA fragmentation. Then fragmented RNA were proceeded with first stand synthesis, second strand synthesis, end repair and A-tailing. Resulting product was ligated with adaptor and selected by size, and next were enriched using PCR. At last DNA purification was performed and samples sent out for sequencing.

treatment_protocol: Pancreatic progenitor stage cells were collected and then mRNA was extracted to proceeded to RNA-seq library preparation.

value: ES-derived pancreatic progenitor cells

tag: es cell line

value: Endocrine

tag: transduction

value: miR-127 at day8 and harvested at day10


title: Hs_H1_WT_D8-10-mIR127_RNAseq_3

tag: cell type


title: BMPR2 wt rep2


title: Hs_H1_WT_D8-14-miR-poly_RNAseq_4

description:
RNA-seq of PP cells transduced with poly-mIR vector at day8 and harvested at day14
day14_poly_ev_all_samples_combat.txt


title: Hs_H1_WT_D8-14-miR-poly_RNAseq_2

value: poly-mIR vector at day8 and harvested at day14


title: Hs_H1_WT_D8-14-miR-poly_RNAseq_3


title: Hs_H1_WT_D8-10-EV_RNAseq 1

description:
RNA-seq of PP cells transduced with empty vector control at day8 and harvested at day10
mir127_FPKM_log2_nozeros.txt


title: Hs_H1_WT_D8-10-EV_RNAseq 2

value: empty vector control at day8 and harvested at day10


title: Hs_H1_WT_D8-10-EV_RNAseq 3


title: Hs_H1_WT_D8-14-miR-poly_RNAseq_1


title: Hs_H1_WT_D8-14-EV_RNAseq_3

description:
RNA-seq of PP cells transduced with empty vector control at day8 and harvested at day14
day14_poly_ev_all_samples_combat.txt


title: Hs_H1_WT_D8-14-EV_RNAseq_4

value: empty vector control at day8 and harvested at day14


title: Hs_H1_WT_D8-10-Let-7g_RNAseq_3

description:
RNA-seq of PP cells transduced with Let-7g loop mutant at day8 and harvested at day10-replicate3.
Endocrine tissue
processed data file: PE_day10_rpkm_values.txt

data_processing:
Reads were aligned to the hg19 by STAR with parameters: --outSAMstrandField intronMotif --outFilterMultimapNmax 1 --runThreadN 5. Only the reads aligned uniquely to one genomic location were retained for subsequent analysis.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Cufflink.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: PE_day10_rpkm_values.txt: Gene expression (RPKM) data table in tab-delimited text format.

extract_protocol:
mRNA was extracted using miRNeasy mini kit from Qiagen.
Libraries were prepared using the protocol from Dr. Sander lab. Briefly, RNA were first poly A selected and then subject to RNA fragmentation. Then fragmented RNA were proceeded with first stand synthesis, second strand synthesis, end repair and A-tailing. Resulting product was ligated with adaptor and selected by size, and next were enriched using PCR. At last DNA purification was performed and samples sent out for sequencing.

value: Let-7g loop mutant at day8


title: Hs_H1_WT_D8-10-miR-poly_RNAseq_3

description:
RNA-seq of PP cells transduced with Poly-miR at day8 and harvested at day10-replicate3.
Endocrine tissue
processed data file: PE_day10_rpkm_values.txt

value: Poly-miR at day8


title: Hs_H1_WT_D8-14-EV_RNAseq_2


title: Hs_H1_WT_D8-10-Let-7a_RNAseq_3

description:
RNA-seq of PP cells transduced with Let-7a loop mutant at day8 and harvested at day10-replicate3.
Endocrine tissue
processed data file: PE_day10_rpkm_values.txt

value: Let-7a loop mutant at day8


title: Hs_H1_WT_D8-14-EV_RNAseq_1


title: Hs_H1_WT_D8-10-miR-375_RNAseq_3

description:
RNA-seq of PP cells transduced with miR-375 at day8 and harvested at day10-replicate3.
Endocrine tissue
processed data file: PE_day10_rpkm_values.txt

value: miR-375 at day8


title: Hs_H1_WT_D8-10-miR-200a_RNAseq_3

description:
RNA-seq of PP cells transduced with miR-200a at day8 and harvested at day10-replicate3.
Endocrine tissue
processed data file: PE_day10_rpkm_values.txt

value: miR-200a at day8